realign 输出结果
目录概览
SAW realign 分析任务通常在工作目录下开启，在该目录下，将找到一个名为 --id 或 --sn（当--id参数没有启用时）的文件夹。输出结果依据数据类型被分类，主要文件被保存在 /outs下。
分析流程输出的具体文件取决于：
- SAW软件的版本
- 分析流程的选择，
SAW count或SAW realign - 是否加入显微镜图像进行分析
- 特定的分析参数设置
- ...
输出文件列表
完成 Stereo-seq T FF 和 Stereo-seq N FFPE 组织样本的 SAW realign 分析任务后，可以在 outs/ 目录下找到以下文件：
| Directory/File Name | Description |
|---|---|
bam/ |
Files in BAM format. |
annotated_bam/ |
BAM file after alignment and annotation. |
<SN>.*.bam |
Indexed BAM file containing position-sorted reads mapped to CIDs, aligned to the genome, and annotated with GTF/GFF. |
<SN>.*.bam.csi |
Index for <SN>.*.bam. |
image/ |
Images are generated from automatic or manual workflows. |
<SN>_<stainType>_regist.tif |
The panoramic image aligned with raw.gef matrix. |
<SN>_<stainType>_tissue_cut.tif |
The tissue segmentation image, based on the aligned panoramic image. |
<SN>_<stainType>_mask.tif |
The cell segmentation image, based on the aligned panoramic image. |
<SN>_<stainType>_mask_edm_dis_<distance>.tif |
The adjusted image, based on the cell segmentation image |
feature_expression/ |
Feature expression matrices in HDF5 format at different dimensions. |
<SN>.raw.gef |
Feature expression matrix includes the whole information over a complete chip region. It only has bin1 expression counts. |
<SN>.tissue.gef |
Feature expression matrix under the tissue coverage region. It is also a visualization GEF which includes expression counts for bin1, 5, 10, 20, 50, 100, 150, 200. |
<SN>.cellbin.gef |
Cellbin feature expression matrix records the information of cells individually, including the centroid coordinate, boundary coordinates, expression of genes, and cell area. |
<SN>.adjusted.cellbin.gef |
Cellbin expression matrix with cell border expanding, based on <SN>_<stain_type>_mask_edm_dis_<distance>.tif. |
<SN>.merge.barcodeReadsCount.txt |
A mapped CID list file with read counts for each CID, including three columns (x, y, count). |
<SN>_raw_barcode_gene_exp.txt |
An annotated list file with the information of coordinate, gene, MID, read counts, which is prepared to be a sampling file that performs sequence saturation. |
analysis/ |
Secondary analysis files. |
<SN>.bin200_1.0.h5ad |
An AnnData H5AD records preprocessing, filtering, normalization, dimensionality reduction, clustering and differential expression analysis, based on This output H5AD is named in the format of |
bin200_marker_features.csv |
Format-integrated differential expression analysis results, using <SN>.tissue.gef of bin200. |
<SN>.cellbin_1.0.h5ad |
An AnnData H5AD records preprocessing, filtering, normalization, dimensionality reduction, clustering and differential expression analysis, using <SN>.cellbin.gef. |
cellbin_marker_features.csv |
Format-integrated differential expression analysis results, using <SN>.cellbin.gef. |
<SN>.cellbin_1.0.adjusted.h5ad |
An AnnData H5AD records preprocessing, filtering, normalization, dimensionality reduction, clustering and differential expression analysis, using <SN>.adjusted.cellbin.gef. |
cellbin_adjusted_marker_features.csv |
Format-integrated differential expression analysis results, using <SN>.adjusted.cellbin.gef. |
<SN>.report.tar.gz |
Analysis summary report of metrics and plots in HTML format. |
report.html |
HTML file, involved in <SN>.report.tar.gz. |
visualization.tar.gz |
StereoMap visualization file to presentation and manual processing. |
<SN>.stereo |
A manifest file in JSON format includes experiment and pipeline information, basic analysis statistics, and references to image and spatial matrix files in the SAW output visualization file folder. |
表达矩阵相关的数据和结果来自于上一次 SAW count 的输出，通过--count-data参数传递信息。
visualization.tar.gz
可视化压缩文件内集成了 StereoMap 展示所需的文件，一个解压后的示例文件如下：
visualization
├── C04144D5.adjusted.cellbin.gef
├── C04144D5.bin200_1.0.h5ad
├── C04144D5.cellbin_1.0.adjusted.h5ad
├── C04144D5.rpi
├── ssDNA_matrix_template.txt
├── C04144D5_SC_20240509_174202_4.0.0.tar.gz
├── C04144D5.stereo
└── C04144D5.tissue.gef
.stereo
.stereo 是一个JSON格式的统领文件，里面记录了：
- SAW分析流程的基本信息
- 组织样本的相关信息
- 基本分析统计结果
- StereoMap所需的图像相关和矩阵相关的文件信息
*文件详细介绍在 “输出结果” 下的各部分说明中可以找到